The main goal of this study was to estimate inflows to the Maranhão reservoir, southern Portugal, using two distinct modeling approaches: a one-dimensional convolutional neural network (1D-CNN) model and a physically based model. The 1D-CNN was previously trained, validated, and tested in a sub-basin of the study area where observed streamflow values were available. The trained model was here subject to an improvement and applied to the entire watershed by replacing the forcing variables (accumulated and delayed precipitation) to make them correspond to the values of the entire watershed. The same way, the physically based MOHID-Land model was calibrated and validated for the same sub-basin, and the calibrated parameters were then applied to the entire watershed. Inflow values estimated by both models were validated considering a mass balance at the reservoir. The 1D-CNN model demonstrated a better performance in simulating daily values, peak flows, and the wet period. The MOHID-Land model showed a better performance in estimating streamflow values during dry periods and for a monthly analysis. Hence, results show the adequateness of both modeling solutions for integrating a decision support system aimed at supporting decision-makers in the management of water availability in an area subjected to increasing scarcity.